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AI agent for chemists

Synthesis Route Planning Agent

A ranked set of practical synthesis routes

Synthesis Route Planning Agent: what goes in, what the agent does and what you get

What it does

Planning a synthesis means choosing steps, reagents and conditions that work together, and a route that looks good on paper can fail on a missing reagent. When a new target is requested, this agent runs a retrosynthesis search and finds literature precedents for each step. It checks reagent availability and price with the chemist's suppliers, flags hazardous or restricted reagents, and catches steps that clash with protecting groups. It then checks whether at least one route passes every check. If none does, it relaxes only the constraints the chemist allows and searches again. It ranks routes by number of steps, cost and strength of precedent, preferring in-stock reagents, and writes a summary. The chemist chooses the route. Edge case: a step backed by only one weak literature example is labeled risky.

How it works

Follow the arrows from top to bottom. The orange dashed arrow is the loop: when a check fails, the agent goes back and tries again.

Start and resultWhat it doesA check on its own workWaits for your OKGoes back and retries
Yes, continueApprovedNo 1 STARTS WHEN New target requested 2 USES A TOOL Run retrosynthesis search 3 USES A TOOL Find literature precedents for each step 4 USES A TOOL Check reagent availability and hazards 5 CHECKS THE RESULT Is there at least one route that passes all checks? If not: relax allowed constraints and search again. Backto step 2. 6 DOES Rank routes and write summary 7 YOU APPROVE Chemist chooses route 8 RESULT Route plan saved
Read the steps as a list
  1. New target requested
  2. Run retrosynthesis search
  3. Find literature precedents for each step
  4. Check reagent availability and hazards
  5. Is there at least one route that passes all checks?If not: relax allowed constraints and search again. Back to step 2.
  6. Rank routes and write summary
  7. Chemist chooses routeThe agent waits here for your OK.
  8. Route plan saved

How it decides

It ranks routes by step count, reagent availability, cost, hazards and strength of precedent.

  • Label steps with weak precedent as risky
  • Flag reagents on the restricted list
  • Prefer routes with in-stock reagents

Make it yours

Every agent is a starting point. You choose these settings for your own situation.

  • Max steps
  • Restricted reagents list
  • Suppliers
  • Cost weight

What keeps you in control

It always asks you first

  • Ordering reagents
  • Using restricted reagents

Hard limits

  • Never orders reagents

It stops when

  • Done: routes delivered
  • Stop: no route found; report

Set it up

We guide you through the set-up, step by step

Members get the full set-up guide for this agent. No technical skills needed: you copy, paste and upload.

10 minto set it up in your AI
5 AIsChatGPT, Claude, Copilot, Gemini, Grok
  • One set of instructions to paste into your AI, with the clicks for ChatGPT, Claude, Microsoft 365 Copilot, Gemini and Grok
  • The agent then walks you through connecting your own data, one source at a time
  • A downloadable copy with the flow chart, the rules and the full guide
Get access to this agent

An example run

What happensA chemist requests a route to a new amide target. The search returns 6 routes. The agent finds literature for most steps and checks reagent stock and hazards. The check fails for all routes on the first pass: each uses a banned reagent or an unavailable building block. The agent searches again with those excluded and finds 2 routes that pass. The chemist chooses the 4-step route.

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